Lisa, there isn't unfortunately a hard and fast rule for the length of DNA used in co-crystallisation. It usually is just a case of screening different lengths, permuting the sequence, and investigating overhangs or gaps in the DNA duplex. We generally work with oligos between 8 and 21 nts in length, but there are many examples of longer DNAs being co-crystallised, the nucleosome comes to mind as an extreme example.
Do you know if the protein binds better to DNA containing secondary structure elements, such as hairpin loops? This can make a difference, especially when you don't have sequence-specificity.
Tony O.
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On 15 Feb 2012, at 08:07, "LISA" <[log in to unmask]> wrote:
> Hi all,
>
> I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA with my protein. But neither of them has good diffraction. Some biochemical data said the longer of DNA, the tigher of the binding betwwen DNA and my protein. The binding is not sequence-specfic. Does anyone have suggestion of the optimization? What is the good length of DNA for crystallization?
> Thank you.
>
> Lisa
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